title: The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs.
abstract: The transcriptome, as the pool of all transcribed elements in a given cell, is regulated by the interaction between different molecular levels, involving epigenetic, transcriptional, and post-transcriptional mechanisms. However, many previous studies investigated each of these levels individually, and little is known about their interdependency. We present a systems biology study integrating mRNA profiles with DNA-binding events of key cardiac transcription factors (Gata4, Mef2a, Nkx2.5, and Srf), activating histone modifications (H3ac, H4ac, H3K4me2, and H3K4me3), and microRNA profiles obtained in wild-type and RNAi-mediated knockdown. Finally, we confirmed conclusions primarily obtained in cardiomyocyte cell culture in a time-course of cardiac maturation in mouse around birth. We provide insights into the combinatorial regulation by cardiac transcription factors and show that they can partially compensate each other's function. Genes regulated by multiple transcription factors are less likely differentially expressed in RNAi knockdown of one respective factor. In addition to the analysis of the individual transcription factors, we found that histone 3 acetylation correlates with Srf- and Gata4-dependent gene expression and is complementarily reduced in cardiac Srf knockdown. Further, we found that altered microRNA expression in Srf knockdown potentially explains up to 45% of indirect mRNA targets. Considering all three levels of regulation, we present an Srf-centered transcription network providing on a single-gene level insights into the regulatory circuits establishing respective mRNA profiles. In summary, we show the combinatorial contribution of four DNA-binding transcription factors in regulating the cardiac transcriptome and provide evidence that histone modifications and microRNAs modulate their functional consequence. This opens a new perspective to understand heart development and the complexity cardiovascular disorders.
authors.affiliation: Group Cardiovascular Genetics, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Jenny
authors.initials: J
authors.lastname: Schlesinger
authors.forename: Markus
authors.initials: M
authors.lastname: Schueler
authors.forename: Marcel
authors.initials: M
authors.lastname: Grunert
authors.forename: Jenny J
authors.initials: JJ
authors.lastname: Fischer
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.forename: Tammo
authors.initials: T
authors.lastname: Krueger
authors.forename: Martin
authors.initials: M
authors.lastname: Lange
authors.forename: Martje
authors.initials: M
authors.lastname: Tönjes
authors.forename: Ilona
authors.initials: I
authors.lastname: Dunkel
authors.forename: Silke R
authors.initials: SR
authors.lastname: Sperling
mesh_terms: D000107:Acetylation; D000818:Animals; D001665:Binding Sites; D050991:GATA4 Transcription Factor / Q000378:metabolism; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D053263:Gene Regulatory Networks; D006657:Histones / Q000378:metabolism*; D000072576:Homeobox Protein Nkx-2.5; D018398:Homeodomain Proteins / Q000378:metabolism; D006801:Humans; D064326:MEF2 Transcription Factors; D051379:Mice; D035683:MicroRNAs / Q000378:metabolism*; D009206:Myocardium / Q000378:metabolism*; D018006:Myogenic Regulatory Factors / Q000378:metabolism; D011485:Protein Binding; D011499:Protein Processing, Post-Translational / Q000235:genetics*; D015203:Reproducibility of Results; D026362:Serum Response Factor / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D050991:GATA4 Transcription Factor; D006657:Histones; D000072576:Homeobox Protein Nkx-2.5; D018398:Homeodomain Proteins; D064326:MEF2 Transcription Factors; C578036:Mef2a protein, mouse; D035683:MicroRNAs; D018006:Myogenic Regulatory Factors; C484469:Nkx2-5 protein, mouse; D026362:Serum Response Factor; D014157:Transcription Factors